Channelrhodopsin-2 and optical control of excitable cells.

abstract：:The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease...

journal_title：Nature methods

authors： Chavez A,Scheiman J,Vora S,Pruitt BW,Tuttle M,P R Iyer E,Lin S,Kiani S,Guzman CD,Wiegand DJ,Ter-Ovanesyan D,Braff JL,Davidsohn N,Housden BE,Perrimon N,Weiss R,Aach J,Collins JJ,Church GM

更新日期：2015-04-01 00:00:00

abstract：:Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are be...

journal_title：Nature methods

authors： Fenno LE,Mattis J,Ramakrishnan C,Hyun M,Lee SY,He M,Tucciarone J,Selimbeyoglu A,Berndt A,Grosenick L,Zalocusky KA,Bernstein H,Swanson H,Perry C,Diester I,Boyce FM,Bass CE,Neve R,Huang ZJ,Deisseroth K

更新日期：2014-07-01 00:00:00

abstract：:Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

journal_title：Nature methods

authors： Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

更新日期：2014-08-01 00:00:00

abstract：:Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant t...

journal_title：Nature methods

authors： McKinney SA,Murphy CS,Hazelwood KL,Davidson MW,Looger LL

更新日期：2009-02-01 00:00:00

abstract：:Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-s...

journal_title：Nature methods

authors： Li B,Gould J,Yang Y,Sarkizova S,Tabaka M,Ashenberg O,Rosen Y,Slyper M,Kowalczyk MS,Villani AC,Tickle T,Hacohen N,Rozenblatt-Rosen O,Regev A

更新日期：2020-08-01 00:00:00

abstract：:Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We...

journal_title：Nature methods

authors： Alley EC,Khimulya G,Biswas S,AlQuraishi M,Church GM

更新日期：2019-12-01 00:00:00

abstract：:All-optical electrophysiology-spatially resolved simultaneous optical perturbation and measurement of membrane voltage-would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond r...

journal_title：Nature methods

authors： Hochbaum DR,Zhao Y,Farhi SL,Klapoetke N,Werley CA,Kapoor V,Zou P,Kralj JM,Maclaurin D,Smedemark-Margulies N,Saulnier JL,Boulting GL,Straub C,Cho YK,Melkonian M,Wong GK,Harrison DJ,Murthy VN,Sabatini BL,Boyden ES,C

更新日期：2014-08-01 00:00:00

abstract：:Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sam...

journal_title：Nature methods

authors： Diep D,Plongthongkum N,Gore A,Fung HL,Shoemaker R,Zhang K

更新日期：2012-02-05 00:00:00

abstract：:Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...

journal_title：Nature methods

authors： Grüner BM,Schulze CJ,Yang D,Ogasawara D,Dix MM,Rogers ZN,Chuang CH,McFarland CD,Chiou SH,Brown JM,Cravatt BF,Bogyo M,Winslow MM

更新日期：2016-10-01 00:00:00

abstract：:Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...

journal_title：Nature methods

authors： Pei Y,Tuschl T

更新日期：2006-09-01 00:00:00

abstract：:Glial cells have been identified as key signaling components in the brain; however, methods to investigate their structure and function in vivo have been lacking. Here, we describe a new, highly selective approach for labeling astrocytes in intact rodent neocortex that allows in vivo imaging using two-photon microscop...

journal_title：Nature methods

authors： Nimmerjahn A,Kirchhoff F,Kerr JN,Helmchen F

更新日期：2004-10-01 00:00:00

abstract：:The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain dif...

journal_title：Nature methods

authors： Chae PS,Rasmussen SG,Rana RR,Gotfryd K,Chandra R,Goren MA,Kruse AC,Nurva S,Loland CJ,Pierre Y,Drew D,Popot JL,Picot D,Fox BG,Guan L,Gether U,Byrne B,Kobilka B,Gellman SH

更新日期：2010-12-01 00:00:00

abstract：:Circuit mapping requires knowledge of both structural and functional connectivity between cells. Although optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactiv...

journal_title：Nature methods

authors： Berlin S,Carroll EC,Newman ZL,Okada HO,Quinn CM,Kallman B,Rockwell NC,Martin SS,Lagarias JC,Isacoff EY

更新日期：2015-09-01 00:00:00

abstract：:We established a conditional site-specific recombination system based on dimerizable Cre recombinase-mediated recombination in the apicomplexan parasite Toxoplasma gondii. Using a new single-vector strategy that allows ligand-dependent, efficient removal of a gene of interest, we generated three knockouts of apicomple...

journal_title：Nature methods

authors： Andenmatten N,Egarter S,Jackson AJ,Jullien N,Herman JP,Meissner M

更新日期：2013-02-01 00:00:00

abstract：:We developed a quantitative PCR method featuring a reusable single-cell cDNA library immobilized on beads for measuring the expression of multiple genes in a single cell. We used this method to analyze multiple cDNA targets (from several copies to several hundred thousand copies) with an experimental error of 15.9% or...

journal_title：Nature methods

authors： Taniguchi K,Kajiyama T,Kambara H

更新日期：2009-07-01 00:00:00

abstract：:Using a line-scanning method during functional magnetic resonance imaging (fMRI), we obtained high temporal (50-ms) and spatial (50-μm) resolution information along the cortical thickness and showed that the laminar position of fMRI onset coincides with distinct neural inputs in rat somatosensory and motor cortices. T...

journal_title：Nature methods

authors： Yu X,Qian C,Chen DY,Dodd SJ,Koretsky AP

更新日期：2014-01-01 00:00:00

abstract：:CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome pro...

journal_title：Nature methods

authors： Datlinger P,Rendeiro AF,Schmidl C,Krausgruber T,Traxler P,Klughammer J,Schuster LC,Kuchler A,Alpar D,Bock C

更新日期：2017-03-01 00:00:00

abstract：:The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sens...

journal_title：Nature methods

authors： Thestrup T,Litzlbauer J,Bartholomäus I,Mues M,Russo L,Dana H,Kovalchuk Y,Liang Y,Kalamakis G,Laukat Y,Becker S,Witte G,Geiger A,Allen T,Rome LC,Chen TW,Kim DS,Garaschuk O,Griesinger C,Griesbeck O

更新日期：2014-02-01 00:00:00

abstract：:Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and pathological associations. The inability to image EVs in fixed tissues has been a major limitation to understanding their role in healthy and diseased tissue microenvironments. Here, we show that crosslinking mammalian tis...

journal_title：Nature methods

authors： Gupta MP,Tandalam S,Ostrager S,Lever AS,Fung AR,Hurley DD,Alegre GB,Espinal JE,Remmel HL,Mukherjee S,Levine BM,Robins RP,Molina H,Dill BD,Kenific CM,Tuschl T,Lyden D,D'Amico DJ,Pena JTG

更新日期：2019-12-01 00:00:00

abstract：:Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very larg...

journal_title：Nature methods

authors： Phanstiel DH,Brumbaugh J,Wenger CD,Tian S,Probasco MD,Bailey DJ,Swaney DL,Tervo MA,Bolin JM,Ruotti V,Stewart R,Thomson JA,Coon JJ

更新日期：2011-09-11 00:00:00

abstract：:The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be cova...

journal_title：Nature methods

authors： Chen F,Wassie AT,Cote AJ,Sinha A,Alon S,Asano S,Daugharthy ER,Chang JB,Marblestone A,Church GM,Raj A,Boyden ES

更新日期：2016-08-01 00:00:00

abstract：:X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize. ...

journal_title：Nature methods

authors： Marx V

更新日期：2014-09-01 00:00:00

abstract：:Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...

journal_title：Nature methods

authors： Campos LA,Liu J,Wang X,Ramanathan R,English DS,Muñoz V

更新日期：2011-02-01 00:00:00

abstract：:The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstr...

journal_title：Nature methods

authors： Biteen JS,Thompson MA,Tselentis NK,Bowman GR,Shapiro L,Moerner WE

更新日期：2008-11-01 00:00:00

abstract：:Optical studies have revealed that, after binding, virions move laterally on the plasma membrane, but the complexity of the cellular environment and the drawbacks of fluorescence microscopy have prevented access to the molecular dynamics of early virus-host couplings, which are important for cell infection. Here we pr...

journal_title：Nature methods

authors： Kukura P,Ewers H,Müller C,Renn A,Helenius A,Sandoghdar V

更新日期：2009-12-01 00:00:00

abstract：:We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and...

journal_title：Nature methods

authors： Corces MR,Trevino AE,Hamilton EG,Greenside PG,Sinnott-Armstrong NA,Vesuna S,Satpathy AT,Rubin AJ,Montine KS,Wu B,Kathiria A,Cho SW,Mumbach MR,Carter AC,Kasowski M,Orloff LA,Risca VI,Kundaje A,Khavari PA,Montine TJ,

更新日期：2017-10-01 00:00:00

abstract：:We describe a GFP-based RNA reporter system (lambdaN-GFP) to visualize RNA molecules in live mammalian cells. It consists of GFP fused to an arginine-rich peptide derived from the phage lambda N protein, lambdaN22, which binds a unique minimal RNA motif and can be used to tag any RNA molecule. LambdaN-GFP uses a small...

journal_title：Nature methods

authors： Daigle N,Ellenberg J

更新日期：2007-08-01 00:00:00

abstract：:The mechanical properties of the cellular microenvironment and their spatiotemporal variations are thought to play a central role in sculpting embryonic tissues, maintaining organ architecture and controlling cell behavior, including cell differentiation. However, no direct in vivo and in situ measurement of mechanica...

journal_title：Nature methods

authors： Serwane F,Mongera A,Rowghanian P,Kealhofer DA,Lucio AA,Hockenbery ZM,Campàs O

更新日期：2017-02-01 00:00:00

abstract：:An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2006-11-01 00:00:00

abstract：:High-resolution optical imaging is critical to understanding brain function. We demonstrate that three-photon microscopy at 1,300-nm excitation enables functional imaging of GCaMP6s-labeled neurons beyond the depth limit of two-photon microscopy. We record spontaneous activity from up to 150 neurons in the hippocampal...

journal_title：Nature methods

authors： Ouzounov DG,Wang T,Wang M,Feng DD,Horton NG,Cruz-Hernández JC,Cheng YT,Reimer J,Tolias AS,Nishimura N,Xu C

更新日期：2017-04-01 00:00:00